The Lonely Angel's Thesis
by Ashura5000
Summary: The Doctor and Amy Pond arrive in the year 2015 AD- but something is wrong. The world is ruined by an event called the Second Impact and humanity is fighting against Angels. Can the Doctor save this day? Crossover- Doctor Who/Evangelion.


The Lonely Angels Thesis

(The following story is a crossover between Doctor Who and Neon Genesis Evangelion. If you don't like crossovers, don't read. Otherwise, please be constructive and open minded as these two worlds collide in what I hope is a logical way.)

Thankyou :)

Doctor Who and Neon Genesis Evangelion are copywrited to there respective owners.

This story takes place before Vincent and the Doctor and before Episode 24 of Neon Genesis Evangelion.

Chapter 1:

It was the sound of the Universe.

A gentle whirring, rising and falling in tempo, at the same moment as a space in time that had previously been completely unoccupied was suddenly full with a half visible object. A gentle hint of blue would have perhaps been seen by normal people, before the perception filter activated, and then the rest of the blue box would have appeared and become part of events forever.

This was a spaceship. This was a Time Machine.

It was the TARDIS and it was the last home for the one, the only, and the greatest mad man to ever own a box in the history of everything past, present, future and sideways.

The door's were flung open excitedly and the man peered his head outside, expecting something and finding nothing, but his joy never left his face and he stepped outside carefully but with a craziness that was being held at bay despite that tiny little impulse in the back of his mind.

He was the Doctor. The one, the only and the best.

"Right, so, future. Future earth, future people, future events. Nothing here, might I add and imagine will probably turn your future upside down if you learned too much, but at the same time it's the future and so you can be awestruck and happy and we appear to be in a broom cupboard of all places?"

The Doctor glanced around in a franticly manic manner, his body whirling on the spot out of both confusion and curiosity. Like a lost puppy he was that, for a moment, he didn't notice his plucky young companion, Amelia- Amy- Pond, until she coughed loudly and put her hands on her hips.

"All of time and space, anything that happened or ever will is what I was promised... And you've brought me to a cupboard?"

The fiery red head stared at the man who had whisked her away in the middle of the night, in an outfit she had plucked from the TARDIS wardrobe (choosing to ignore the fact that the Doctor, for some reason, had women's clothing stashed away) and stared impatiently at the young, mad, fellow from her childhood (known as the Raggedy Doctor back then) tried to explain where they were and how it could perhaps possibly be the greatest place in the entire universe.

"Look, yes, I know. I promised you adventure and fun and crazy adventures as we ran through time and space being sort of brilliant. So, before we jump to conclusions," He opened the door, noting with annoyance that it squeaked loudly; "Let's take a look outside, hmm?"

Letting his companion go ahead of him and closing the TARDIS door with a snap of his fingers, the pair entered the hallway of the strange building. The walls were white, some were grey, and the ground was squeaky clean and otherwise completely dull and boring.

"Ah, yes, this is rather boring."

"Are you going to become Mr. Grumpy face again? I thought you just said we should look outside."

"That was then and was before I got bored. I rather dislike being bored, it makes me slow and..." He waved his hands and completely lost the trail of his thoughts, instead choosing to instead point at the distance and walk along.

The lack of windows in this place troublesome, making the Doctor question exactly where they were, and although he was tempted to taste the walls with his Time Lord tongue and deduce whether or not they were from Earth or some other planet (and then, how long the building had been standing), his mind was drawn back to a comment made by Amy before Rory... Back then, with the Silurians, had made him more self conscious about this talent. So he continued to hope, to see if something would catch there eye and make this perhaps an interesting curious place to be in in his further attempts of making the young girl happy and to avoid that strange depression she sometimes seemed to feel, despite not knowing-

"That signs in Japanese!" Amy cried suddenly, pointing up at, sure enough, a sign that pointed in various general directions.

"Yeah, it is." The Doctor replied, almost amazed that it mattered so much to the girl, until he remembered-

"I cant _READ_ Japanese!"

"Oh, right, well. Now you can! Congratulations. This is a special day and to reward this most amazing of talents I shall take you for sushi since we appear to be in..." He ran his finger through the air as though searching for dust, prompting a look of confusion from Amelia, "...A building that appears to have been made by Japanese people. Funny that."

"Did the Japanese sign tip you off?"  
"Funnily enough, it did. Plus I can taste and identify the race of the people occupying wherever this building is through the individual dead cells that are floating around us and _yes_ I know that's disgusting. Now then, Pond, can you inform me as to what such a sign says?"

Amy turned, opting to avoid dwelling on the matter of the Time Lord's taste, and gazed up at the weird black with white kanji sign, finding her vision strangely effected by the writing. It was as though one eye was reading the kanji and the other side had decided it to read the same thing in perfect English. Yet, somehow, she didn't feel dizzy or disturbed. If anything, it made complete sense to her.

She read, and to her dismay it wasn't some crazy in depth Japanese slogan about honouring yourself or how to learn Karate or find inner peace in twelve easy steps as she had been brought up with thanks to those weird foreign films her Aunt had shown her growing up, but was in fact merely talking about the directions to the main office, the second floor and...

"Control centre? I like a good old control centre, me." The Doctor said, pulling out his Sonic Screwdriver and running it along the wall before flicking it back and checking the readings. The wall's were strong, maybe they were in space...?

He scanned the sign. At his age he no longer saw the blurry faded change of High Gallifreyan or English. In fact, with over 900 (or more, he couldn't quite recall) years to his lifespan (in Earth years, at least) he was pretty much fluent in such languages now anyway. But that word, that word just before control centre. That had its bases in Greece way before the other words had been conceived.

"Magi..." He said curiously as Amy glanced around at the plain and boring corridor, well aware that they were casting an echo and if she had learned anything on her travels it was that they should never be ambushed by adventure. She tried not to say anything, for fear that such terrible adventure would roll up the hallway, but curiosity got the better of her and she spoke in a hushed voice.

"Doctor, what year is this?"  
"I don't know." Was his quick and not so quiet reply, instead adding sharply; "Amy, do you know what the Magi are?"

His companion blinked and the Doctor nodded. She didn't seem to register the word, but she was a 21st Century Earth Girl. Religion held no basis on humanity as much as it once did, although its influences always stretched to the far reaches of the Universe, always asking the great questions.

"The Magi," He started, staring at the sign above them but walking without purpose; "Are in a nutshell the names given to the Three Wise Men. Melchior, Caspar and Balthasar. Those three gentleman who gave presents to Jesus, nice chaps, we had tea, although, of course, what really happened was- Oh!"

He clicked his watch, which circled round at an alarming rate, and he smiled brightly, unaware that Amy's expression was one of confusion.

Her mind was already asking that big question. Why was a control centre named after the Wise Men? What would be the point? It may have been nothing but something had made her stomach uneasy, The Doctor however was smiling as he checked the time and then held up his watch.

"Look at that. It's tea time. Shall we go to the Control Centre and ask for a cuppa, and a Custard Cream, and perhaps-."

The ground shook violently with a powerful force that made the roof, the walls and the ground vibrate incredibly and, to those standing there, feel as though they were being ripped apart. Amy hit the ground instantly, assuming an Earthquake, whilst the Doctor held the wall and glanced around and made the connection instantly. His mind working powerfully to assess the exact location and cause of such a tremor and as always, his mouth worked before his mind;

"That's no earthquake, it's an explosion!" He said, his voice reaching Amy's ears slightly muffled as the bland hallway they were in continued to rumble and the sign fell from its place on the roof and smashed into a thousand pieces.

The Doctor continued to think however, even as his brain glanced at each individual fragment of the sign in turn, and still worked to calculate the exact size and strength of such an explosion. The results making his face turn white and his hearts panic.

The room began to calm after a few more moments, although after tremors continued to make the hallway vibrate, a red light began to flash throughout the hallway, an obvious alert, although the Doctor had a brief flash in his memory and he wondered if it was worth telling his companion about how red was camp and mauve was much more internationally accepted, but then again, with her hair colour... He pressed on.

"Come along now." He said, picking up his partner and brushing down his tweed jacket, "That explosion was several miles above us and I don't mean in the sky. Probably meaning we are underground in some kind of Geofront, which makes sense why no windows, we don't really need to see outside. _But_ that explosion..."

He shook his head, noticed Amy was as white as a sheet, but unfortunately his mouth spoke before his mind could tell him no.

"That explosion was more powerful than a nuclear bomb. More powerful than several. Which means that we may be in the middle of a war."

"Doctor." Amy said calmly, "Can we not stay here? I've seen enough wars in the past, I don't want to see how we kill ourselves in the future as well."

It was a formal request but one unlike anything Amy had ever asked of him before. She had told him after that incident with the star whale how her memory wiped self had wanted to keep him away from doing something terrible, like murdering an innocent and beautiful creature, but this was completely different.

That explosion had shaken her, completely. Had she sensed the malice behind it like he had? Or perhaps she knew she didn't want to see innocents die.

Innocents like Rory.

Poor Rory.

He repressed the memory and smiled at her. He was going to be kind for once.

"Yeah. We will leave. Maybe one day we'll return, but for now, I think it's best that we-."

He froze mid sentence, cursing in his mind.

"There are guards behind us, with guns, right?" Amy asked with a long, deep, sigh. It was always the way, it seemed.

"Well, not guards per say. Men in matching uniforms holding guns. More like soldiers. But yes the point is, they are holding weapons and the one on the left is clearly the leader and he is approaching us."

So he did. In fact, the middle aged soldier pushed Amy into the Doctor's arms, held up his gun and snapped angrily; "You two! Who are you! You're not staff, so where's your identification?"

Well he certainly had the stereotypical angry panicked soldier role down...

A sudden flash of anger hit the Time Lord, regarding the way his companion had been so poorly treated, but the Doctor responded and later, in hindsight, he would regard it as possibly the wrong way to fix the situation.

"In order then, since you asked so nicely. Yes there are two of us, can we get some tea? Also, we are travellers and are not staff. So my identification is probably not existent."

He seemed quite pleased with himself, until Amy tugged his arm and whispered into his ear; "Or, alternatively, psychic paper?"

Judging by the slow loading of guns and the angered faces of the men and women before them, the Doctor got the impression from his companion and his own angry brain that maybe he should have tried that option.

The soldiers however, decked out in pale, bland, camouflage that fit in exceptionally well with the already boring surroundings of the hallway (truly, they were invisible) held up there guns as though thoroughly prepared to shoot and kill the two mysterious strangers.

But in his mind he saw it. The way they held the guns sloppily, the fact that one of the guns wasn't even loaded properly and the other had its safety turned off. These people were not soldiers per say, nor guards, they looked and acted more like the kind of police officers who hung around at a mall. No formal training, they were just there for show and would perhaps be utterly useless in a real fight.

Amy, however, didn't see this as clearly as the Doctor. She saw a group of men and women, one leader who was angry and the others quite timid. She saw a way out, a strange way, but it was one she hadn't used since she'd met the Doctor...

"Look, fine, you got us. Congratulations."

"Amy, please, don't tease the gentleman."

"Oh come off it Doctor, the jig is up."

"The jig? Are we dancing? It's been a while since I last-"

"Would you two knock off the talking!" Snapped the lead guard, but Amy had now dropped her hands and glared at him sternly.

"Would you knock off talking _ma'am_, I think you'll find. Now tuck your shirt in and take us to the Magi Central Control room at once. We need to talk to your superiors about the lax security because me and my companion here just waltzed right in."

The Doctor blinked and he almost whirled around and hissed; "I'm the companion?" but he held it back. The Soldiers were taken aback by such a brash statement and whilst Amy hadn't indicated they were a part of the organisation (since the Doctor had already confirmed that), her confidence had set enough doubts into the minds of what may as well be simple civilians.

After a moment of conversing under there breaths, although the Doctor caught every word (something about a battle on the surface and the alleged death of a pilot), the soldiers spoke into a radio, seemed to receive some orders back, before finally turning there guns on to the two mysterious strangers and gave the order.

"Let's go then. We'll take you to see Major Katsuragi, she can decide what she wants to do with you. Although given what has apparently just happened I get the feeling she won't be too pleased..."

The Doctor smiled and made a strong, very important absolutely necessary mental note to use his psychic paper and, hopefully, get Amy off to Reno as soon as possible.

In Amy Pond's eyes, the entire underground base- NERV, the soldiers had called it- was as boring as expected.

Sure, plenty of eye candy, but for some reason her heart wasn't into it. Plus everyone kept staring at the only non-Japanese women and men for possibly miles and she wondered, with a sinking feeling, if perhaps the war was between the American and English forces. Perhaps she'd be executed?

Then again, being Scottish, she'd probably get a pardon. She hoped.

Born in Scotland, raised in England, and always waiting for the Raggedy Doctor to come back and whisk her away after that magical night of fish custard and swimming pool's in the library. He had then jumped five minutes into the future, kind of overshot by twelve years, and then when he had saved the entire planet for what he claimed was the latest of many, he had disappeared for another two.

Then he had taken her across the stars, they had seen Star Whales, Daleks, Weeping Angels, Vampire Fish and Silurians. They had fought the Doctor's dark side, they had had many adventures that were darted around between those previous. It was all a wonderful fabulous blur.

Ahead of her the Doctor made no attempt to turn around and see how she was but she suspected he was going through his own brilliant mind in order to figure a way out. She wondered how many times he had been in a situation like this and also wondered how many of the companions before her had lived to tell the tale.

Frustrated, she shook her head. Death was on her mind and it was beginning to annoy her.

After a few minutes of boring hallways, and entertaining herself by reading the Japanese kanji fluently, the hallways began to widen and the number of soldiers increased. All of them armed and talking, all of them looking depressed.

Had the explosion wiped out many of there soldiers? Had the Doctor brought her to the last days of a war, with the TARDIS locked away in a cupboard?

The soldiers activated a pair of locked doors with there passes, allowed the Time Lord and human to enter, and Amy gasped loudly.

It really was a massive control room. Much larger and less Star Trek than the one aboard the Byzantium, there were men and women all around her working, massive screens with numbers and static, and steps leading up to where the most important people worked. People like this Major Katsuragi person.

If anything, it reminded her of the Cabinet War Rooms more than a control centre, but that probably made sense considering...

"Up you go then, and mind what you say. She's not in a good mood."

The soldiers didn't follow and perhaps this was a trap. Amy had a horrible thought of the pair getting caught in a crossfire and lying dead on the steps.

She'd never have been to Reno, oh the horror!

Damn it, enough death, she scolded herself. The Doctor always protects you and never let's anyone die.

But why didn't she believe that?

However, her brain was once more seeing the worst once more and they did in fact make it to the top of the steps with little to no problems (The Doctor tripped over a step and then acted as though nothing had happened, thus one momentary disaster averted thanks to clever footwork).

They reached the top at last, the screens flashing and voices speaking frantically. Phrases like; "Let's get the team and retrieve the Pilot", "Was the evacuation successful? Where will the civilians go next" and "What's the status of the the First, is-."

The Doctor clapped his hands and held them as he seemed to dart ahead, leaving Amy to continue glancing around completely amazed and lost in the view and the technology and the people staring at them.

"Ah! Hello there. Pleasure to meet you, I'm the Doctor and this is Amy and this is all just brilliant! The combination of steam-punk-like technology combined with an obvious taste of nuclear fusion in the air combined to create a lot of power for a gorgeous computer system and..." He paused and put his hands on a young women's soldiers, who flinched at his touch until she noticed his lack of malice; "Do I detect the slightest hint of a Biological Fusion within that big cluster of machines Miss Ibuki?"

She glanced up at him, her eyes warm but with tears fresh in the corners, tears that he noticed and felt a pang of guilt of not noticing sooner. This was quickly replaced however, as Amy shouted; "Doctor!" and something hard, cold and metal pressed against his back and a quick hand grabbed the back of his tweed jacket and pulled him away from the young worker.

He was whirled around, noticed the small black pistol, and then focused his intention on the strong woman with the Major badges and the dark hair and the killer expression on her face.

"...Cup of tea? No, wait, Japan. Green tea?" He said softly.

"Who are you!" She snapped in response. Clearly the conversation was getting off to a good start.

"I'm the Doctor."

"Your name!"

"The Doctor."

She put the safety off her gun, aimed it directly at the Doctor's head, and spoke slowly.

"I have just lost a Pilot. I am _not_ playing games here. What. Is. Your. Name?"

From the corner of his eye he could see Amy, frozen in spot by a pair of armed guards, or soldiers, or whatever. They were glancing at him and this Major Katsuragi, waiting for the signal to either start shooting or stand down, but fortunately the Time Lord had been in this type of situation before.

"Major Katsuragi?"  
"That's my name!"

He sighed; "No, I was saying your name in order to get your attention. It was a clever little way of letting us eventually build a strong relationship now shut up for a second and let me finish. Do you have records of old military forces? I'm not quite sure where I am and if you could be so kind as to contact UNIT and inform them that the Doctor-."

"UNIT? What is that?" Asked a young man with glasses, turning on his chair to face the situation behind him. He also looked panicked and upset about some event, perhaps the death of this pilot.

"UNIT. The Unified Intelligence Taskforce? Or better yet, contact Torchwood, they can vouch for me-"

These names meant nothing to Amy and, judging by the women's face, they meant nothing to her as well. Emphasised further when she pushed her gun slowly closer to the Doctor's face and squinted at him.

"I don't know what you are playing at, or who you work for-"

"Look, just do a search for the Doctor and you'll find out all you need to know. If it helps, I could talk to the Brigadier- well, his successor- or Captain Jack Harkness, he must be around, he always is. What year is this anyway?"

"What are you rambling on about now?" This was a women in a white coat this time, her hair was blonde and she looked as pale as everyone else, but like the Major she had a sense of authority and anger that made him truly appreciate the idea that a woman scorned could be a terrible thing. On that note, he decided to never make Amy really angry.

"The year. I'm guessing late 24th Century?"

"Doctor..."

"And what planet is this? It could be Earth. But it's possible that this may be a Tokyo moon base? Or a sanctuary base?"

"Doctor..."

"Hang on Amy, I'm busy. Oh! I get it, this Geofront is digging for some crazy mysterious substance and the natives of this planet are angry at you and there is a war going on?"

"Doctor."

"Amy, seriously. Okay! I got it, we aren't actually on a planet or a moon but an asteroid and we are getting bombarded with _other_ explosive asteroids?"

"Doctor!"

"What Amy!" The Doctor rounded at his companion, completely ignoring the confused expressions on Major Katsuragi and the other staff and armed members all around him, who probably regarded this man as completely and utterly insane.

Even more bizarrely was the fact that he was now yelling at his partner in crime, if they were in fact criminals, but the questions he was asking and the words he was saying didn't make sense in context.

The Doctor however had frozen completely, until his hand disappeared into his jacket pocket and before Katsuragi could raise her gun and fire he pulled out a small identification and handed it to her.

"I'm the Doctor. Doctor John Smith. This is my companion, Nurse Amy Pond, and something is terribly wrong here."

The date, written beneath a large clock above them, just above a man who was covering his face with gloved hands and his subordinate standing at his side, read 2015AD.

2015 AD.

Twenty. Fifteen. Anno Domini.

He shoved the psychic paper into Katsuragi's hand and immediately began to whirl around at the computer screens. The dates were the same, the technology was wrong. Completely wrong. A scanner indicated he was on Earth. In fact, the scans revealed he was in Japan, and there was nothing to prove otherwise. The maps looked different, the technology was different...

"Amy this is five years in your future."

"I know that. What's wrong?"

He froze and stared at her. "Five years from now is when we met the Silurians and everything is wrong. It tastes and smells wrong. It can't possibly be 2015AD, the human race can't possibly be in space. Doesn't it look wrong?"

"It's Japan. Everything looks different to me."

The Doctor opened his mouth to say something else, but he froze. They had to get out of this area in order to discuss what had happened, and with armed men and women all around them.

They were both aware that the Katsuragi woman was staring at them, still gazing at the identification- the psychic paper- and back at the two newcomers. She had received the report over the radio, just after the First had- just after the explosion. Two newcomers had entered NERV, both from abroad, and apparently they wanted to meet whoever was in charge.

The Commander would never have met them, instead he probably would have ordered an execution, so she had agreed instead and she fully expected to be the one doing that final dirty deed herself- but now that she was reading this small piece of paper, apparently from the highest authority in all the land, saying that what this strange hyperactive man and his ginger haired friend were...

"Psychologists? For the Pilots?" She stared at them both, aware of the man's panic, aware of the fear he seemed to be exhibiting, aware that he knew something was really wrong.

Had he known Kaji?

"Is that what- Yes, yes. I'm here to analyse and determine the mental state of your Pilots in order to see if they are fit for battle, is that okay?"

Misato Katsuragi threw the paper at him casually, to which he fumbled with his catch, and nodded slowly. She would buy this for now, allow him to do what he needed to do, and when the time was right she would confront him about why he was here. Both of them, in fact.

"I suppose it's fine."

"Major!" Cried Ritsuko Akagi, glaring at her old friend. She couldn't possibly be accepting these explanations, right...?

"It's _fine_ Ritsuko. If the Commander says no, then that's fine and dandy, but the Pilot's need someone to talk to, especially after today."

"What happened today?" Asked the women- the man had called her Amy- stepping forward and glancing at him inquisitively. Was she in the investigation as well?

"We lost a Pilot."

The man- the Doctor, he had called himself- spoke next; "Well it's a war, pilots die all the time, too bad so sad, but it happens."

Perhaps he realised everyone was staring at him with a never before seen blood lust, or perhaps it was the look of his partner that seemed to say; "Don't do that, trust me" but he seemed to nod slowly after a moment and wave his hand.

"Sorry, brain lags behind and mouth goes to fast, I'm working on it but- Yes, anyway, sorry, Pilot deceased."

"You make it sound as if you don't know what's going on here. Surely, as you _broke_ _in_ to this facility, you should have seen what happened up above. With the EVA Unit's and the Angel's?"

This was Ritsuko Akagi this time talking in a harsh tone, clearly she despised this man and the ease in which he had apparently integrated himself into the events. She had heard no word about any Psychologists coming in anyway because it wasn't exactly necessary. The Pilot's had to fight the Angel's and that was _ALL _they had to do.

This other Doctor however seemed to only respond to the word Angel and she could tell that his eyes were imagining things different, as though he had seen other creatures with the same name, but the EVA Unit's held nothing special to him.

"EVA?" Amy asked before the Doctor could even attempt to determine what the future letters could have stood for, but suddenly the screen behind them scrambled, fuzzed even further, and suddenly with a crack footage was restored.

Standing in the midst of a still burning fire that could be seen for miles, Amy thought whilst a chill travelled down her spine, was the shadow of a man.

"No..." Whispered the Doctor as a collected gasp filled the Magi Control Room, clearly they were as shocked as the two newcomers were over the destruction. He continued; "No, it's not a human, look closer and be calm about it."

She did, focusing as hard as she could, and then she could see it. It had a shape of a man, but if you looked past the familiar it was covered in armour, it had a horn and whilst it was charred she could see it was purple.

But what chilled her the most was how it seemed to radiate that it was a conscious, alive, being- whilst also acting like some sort of... Robot?

It was as though it hadn't properly woken up yet, although it could at any moment.

It stood in the fire as it body burned but didn't scream with pain, and Ritsuko Akagi turned to the Doctor and Amelia and shot her hand at the footage.

"That," She said harshly; "Is Evangelion Unit 01."

To Be Continued...

Wahey! I dont know why, but I love this idea.

For the last few years, growing up with Doctor Number Ten, I found myself watching movies and tv shows and something would always cross my mind whether it was a day later, a month later, or whatever. That thing was, how would the story differ if the Doctor was there?

That bieng said, the story of Evangelion, especially towards the end, seemed completely hopeless. Could the Eleventh Doctor perhaps make a difference?

I think so. But let's see. :)


End file.
